2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureColourI;
25 import jalview.datamodel.GraphLine;
26 import jalview.datamodel.features.FeatureAttributes;
27 import jalview.datamodel.features.FeatureAttributes.Datatype;
28 import jalview.datamodel.features.FeatureMatcher;
29 import jalview.datamodel.features.FeatureMatcherI;
30 import jalview.datamodel.features.FeatureMatcherSet;
31 import jalview.datamodel.features.FeatureMatcherSetI;
32 import jalview.gui.JalviewColourChooser.ColourChooserListener;
33 import jalview.schemes.FeatureColour;
34 import jalview.util.ColorUtils;
35 import jalview.util.MessageManager;
36 import jalview.util.matcher.Condition;
38 import java.awt.BorderLayout;
39 import java.awt.Color;
40 import java.awt.Dimension;
41 import java.awt.FlowLayout;
42 import java.awt.GridLayout;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.FocusAdapter;
46 import java.awt.event.FocusEvent;
47 import java.awt.event.ItemEvent;
48 import java.awt.event.ItemListener;
49 import java.awt.event.MouseAdapter;
50 import java.awt.event.MouseEvent;
51 import java.text.DecimalFormat;
52 import java.util.ArrayList;
53 import java.util.List;
55 import javax.swing.BorderFactory;
56 import javax.swing.BoxLayout;
57 import javax.swing.ButtonGroup;
58 import javax.swing.JButton;
59 import javax.swing.JCheckBox;
60 import javax.swing.JComboBox;
61 import javax.swing.JLabel;
62 import javax.swing.JPanel;
63 import javax.swing.JRadioButton;
64 import javax.swing.JSlider;
65 import javax.swing.JTextField;
66 import javax.swing.border.LineBorder;
67 import javax.swing.event.ChangeEvent;
68 import javax.swing.event.ChangeListener;
71 * A dialog where the user can configure colour scheme, and any filters, for one
74 * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
77 public class FeatureTypeSettings extends JalviewDialog
79 private final static String LABEL_18N = MessageManager
80 .getString("label.label");
82 private final static String SCORE_18N = MessageManager
83 .getString("label.score");
85 private static final int RADIO_WIDTH = 130;
87 private static final String COLON = ":";
89 private static final int MAX_TOOLTIP_LENGTH = 50;
91 private static final int NO_COLOUR_OPTION = 0;
93 private static final int MIN_COLOUR_OPTION = 1;
95 private static final int MAX_COLOUR_OPTION = 2;
97 private static final int ABOVE_THRESHOLD_OPTION = 1;
99 private static final int BELOW_THRESHOLD_OPTION = 2;
101 private static final DecimalFormat DECFMT_2_2 = new DecimalFormat(
105 * FeatureRenderer holds colour scheme and filters for feature types
107 private final FeatureRenderer fr; // todo refactor to allow interface type
111 * the view panel to update when settings change
113 final AlignmentViewPanel ap;
115 final String featureType;
118 * the colour and filters to reset to on Cancel
120 private final FeatureColourI originalColour;
122 private final FeatureMatcherSetI originalFilter;
125 * set flag to true when setting values programmatically,
126 * to avoid invocation of action handlers
128 boolean adjusting = false;
131 * minimum of the value range for graduated colour
132 * (may be for feature score or for a numeric attribute)
137 * maximum of the value range for graduated colour
142 * scale factor for conversion between absolute min-max and slider
147 * radio button group, to select what to colour by:
148 * simple colour, by category (text), or graduated
150 JRadioButton simpleColour = new JRadioButton();
152 JRadioButton byCategory = new JRadioButton();
154 JRadioButton graduatedColour = new JRadioButton();
160 JPanel singleColour = new JPanel();
162 JPanel minColour = new JPanel();
164 JPanel maxColour = new JPanel();
166 private JComboBox<String> threshold = new JComboBox<>();
168 JSlider slider = new JSlider();
170 JTextField thresholdValue = new JTextField(20);
172 private JCheckBox thresholdIsMin = new JCheckBox();
174 private GraphLine threshline;
176 private ActionListener featureSettings = null;
178 private ActionListener changeColourAction;
181 * choice of option for 'colour for no value'
183 private JComboBox<String> noValueCombo;
186 * choice of what to colour by text (Label or attribute)
188 private JComboBox<String> colourByTextCombo;
191 * choice of what to colour by range (Score or attribute)
193 private JComboBox<String> colourByRangeCombo;
195 private JRadioButton andFilters;
197 private JRadioButton orFilters;
200 * filters for the currently selected feature type
202 List<FeatureMatcherI> filters;
204 private JPanel chooseFiltersPanel;
212 public FeatureTypeSettings(FeatureRenderer frender, String theType)
215 this.featureType = theType;
217 originalFilter = fr.getFeatureFilter(theType);
218 originalColour = fr.getFeatureColours().get(theType);
225 } catch (Exception ex)
227 ex.printStackTrace();
231 updateColoursPanel();
233 updateFiltersPanel();
237 colourChanged(false);
239 String title = MessageManager
240 .formatMessage("label.display_settings_for", new String[]
242 initDialogFrame(this, true, false, title, 580, 500);
247 * Configures the widgets on the Colours panel according to the current feature
250 private void updateColoursPanel()
252 FeatureColourI fc = fr.getFeatureColours().get(featureType);
255 * suppress action handling while updating values programmatically
263 if (fc.isSimpleColour())
265 singleColour.setBackground(fc.getColour());
266 singleColour.setForeground(fc.getColour());
267 simpleColour.setSelected(true);
271 * colour by text (Label or attribute text)
273 if (fc.isColourByLabel())
275 byCategory.setSelected(true);
276 colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
277 if (fc.isColourByAttribute())
279 String[] attributeName = fc.getAttributeName();
280 colourByTextCombo.setSelectedItem(
281 FeatureMatcher.toAttributeDisplayName(attributeName));
285 colourByTextCombo.setSelectedItem(LABEL_18N);
290 colourByTextCombo.setEnabled(false);
293 if (!fc.isGraduatedColour())
295 colourByRangeCombo.setEnabled(false);
296 minColour.setEnabled(false);
297 maxColour.setEnabled(false);
298 noValueCombo.setEnabled(false);
299 threshold.setEnabled(false);
300 slider.setEnabled(false);
301 thresholdValue.setEnabled(false);
302 thresholdIsMin.setEnabled(false);
307 * Graduated colour, by score or attribute value range
309 graduatedColour.setSelected(true);
310 updateColourMinMax(); // ensure min, max are set
311 colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
312 minColour.setEnabled(true);
313 maxColour.setEnabled(true);
314 noValueCombo.setEnabled(true);
315 threshold.setEnabled(true);
316 minColour.setBackground(fc.getMinColour());
317 maxColour.setBackground(fc.getMaxColour());
319 if (fc.isColourByAttribute())
321 String[] attributeName = fc.getAttributeName();
322 colourByRangeCombo.setSelectedItem(
323 FeatureMatcher.toAttributeDisplayName(attributeName));
327 colourByRangeCombo.setSelectedItem(SCORE_18N);
329 Color noColour = fc.getNoColour();
330 if (noColour == null)
332 noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
334 else if (noColour.equals(fc.getMinColour()))
336 noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
338 else if (noColour.equals(fc.getMaxColour()))
340 noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
344 * update min-max scaling if there is a range to work with,
345 * else disable the widgets (this shouldn't happen if only
346 * valid options are offered in the combo box)
348 scaleFactor = (max == min) ? 1f : 100f / (max - min);
349 float range = (max - min) * scaleFactor;
350 slider.setMinimum((int) (min * scaleFactor));
351 slider.setMaximum((int) (max * scaleFactor));
352 slider.setMajorTickSpacing((int) (range / 10f));
354 threshline = new GraphLine((max - min) / 2f, "Threshold",
356 threshline.value = fc.getThreshold();
358 if (fc.hasThreshold())
360 threshold.setSelectedIndex(
361 fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
362 : BELOW_THRESHOLD_OPTION);
363 slider.setEnabled(true);
364 slider.setValue((int) (fc.getThreshold() * scaleFactor));
365 thresholdValue.setText(String.valueOf(fc.getThreshold()));
366 thresholdValue.setEnabled(true);
367 thresholdIsMin.setEnabled(true);
371 slider.setEnabled(false);
372 thresholdValue.setEnabled(false);
373 thresholdIsMin.setEnabled(false);
375 thresholdIsMin.setSelected(!fc.isAutoScaled());
383 * Configures the initial layout
385 private void initialise()
387 this.setLayout(new BorderLayout());
390 * an ActionListener that applies colour changes
392 changeColourAction = new ActionListener()
395 public void actionPerformed(ActionEvent e)
402 * first panel: colour options
404 JPanel coloursPanel = initialiseColoursPanel();
405 this.add(coloursPanel, BorderLayout.NORTH);
408 * second panel: filter options
410 JPanel filtersPanel = initialiseFiltersPanel();
411 this.add(filtersPanel, BorderLayout.CENTER);
413 JPanel okCancelPanel = initialiseOkCancelPanel();
415 this.add(okCancelPanel, BorderLayout.SOUTH);
419 * Updates the min-max range if Colour By selected item is Score, or an
420 * attribute, with a min-max range
422 protected void updateColourMinMax()
424 if (!graduatedColour.isSelected())
429 String colourBy = (String) colourByRangeCombo.getSelectedItem();
430 float[] minMax = getMinMax(colourBy);
440 * Retrieves the min-max range:
442 * <li>of feature score, if colour or filter is by Score</li>
443 * <li>else of the selected attribute</li>
449 private float[] getMinMax(String attName)
451 float[] minMax = null;
452 if (SCORE_18N.equals(attName))
454 minMax = fr.getMinMax().get(featureType)[0];
458 // colour by attribute range
459 minMax = FeatureAttributes.getInstance().getMinMax(featureType,
460 FeatureMatcher.fromAttributeDisplayName(attName));
466 * Lay out fields for graduated colour (by score or attribute value)
470 private JPanel initialiseGraduatedColourPanel()
472 JPanel graduatedColourPanel = new JPanel();
473 graduatedColourPanel.setLayout(
474 new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
475 JvSwingUtils.createTitledBorder(graduatedColourPanel,
476 MessageManager.getString("label.graduated_colour"), true);
477 graduatedColourPanel.setBackground(Color.white);
480 * first row: graduated colour radio button, score/attribute drop-down
482 JPanel graduatedChoicePanel = new JPanel(
483 new FlowLayout(FlowLayout.LEFT));
484 graduatedChoicePanel.setBackground(Color.white);
485 graduatedColour = new JRadioButton(
486 MessageManager.getString("label.by_range_of") + COLON);
487 graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
488 graduatedColour.setOpaque(false);
489 graduatedColour.addItemListener(new ItemListener()
492 public void itemStateChanged(ItemEvent e)
494 if (graduatedColour.isSelected())
500 graduatedChoicePanel.add(graduatedColour);
502 List<String[]> attNames = FeatureAttributes.getInstance()
503 .getAttributes(featureType);
504 colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
505 colourByRangeCombo.addItemListener(new ItemListener()
508 public void itemStateChanged(ItemEvent e)
515 * disable graduated colour option if no range found
517 graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
519 graduatedChoicePanel.add(colourByRangeCombo);
520 graduatedColourPanel.add(graduatedChoicePanel);
523 * second row - min/max/no colours
525 JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
526 colourRangePanel.setBackground(Color.white);
527 graduatedColourPanel.add(colourRangePanel);
529 minColour.setFont(JvSwingUtils.getLabelFont());
530 minColour.setBorder(BorderFactory.createLineBorder(Color.black));
531 minColour.setPreferredSize(new Dimension(40, 20));
532 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
533 minColour.addMouseListener(new MouseAdapter()
536 public void mousePressed(MouseEvent e)
538 if (minColour.isEnabled())
540 String ttl = MessageManager.getString("label.select_colour_minimum_value");
541 showColourChooser(minColour, ttl);
546 maxColour.setFont(JvSwingUtils.getLabelFont());
547 maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
548 maxColour.setPreferredSize(new Dimension(40, 20));
549 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
550 maxColour.addMouseListener(new MouseAdapter()
553 public void mousePressed(MouseEvent e)
555 if (maxColour.isEnabled())
557 String ttl = MessageManager.getString("label.select_colour_maximum_value");
558 showColourChooser(maxColour, ttl);
562 maxColour.setBorder(new LineBorder(Color.black));
565 * default max colour to last plain colour;
566 * make min colour a pale version of max colour
568 FeatureColourI fc = fr.getFeatureColours().get(featureType);
569 Color bg = fc.getColour() == null ? Color.BLACK : fc.getColour();
570 maxColour.setBackground(bg);
571 minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
573 noValueCombo = new JComboBox<>();
574 noValueCombo.addItem(MessageManager.getString("label.no_colour"));
575 noValueCombo.addItem(MessageManager.getString("label.min_colour"));
576 noValueCombo.addItem(MessageManager.getString("label.max_colour"));
577 noValueCombo.addItemListener(new ItemListener()
580 public void itemStateChanged(ItemEvent e)
586 JLabel minText = new JLabel(
587 MessageManager.getString("label.min_value") + COLON);
588 minText.setFont(JvSwingUtils.getLabelFont());
589 JLabel maxText = new JLabel(
590 MessageManager.getString("label.max_value") + COLON);
591 maxText.setFont(JvSwingUtils.getLabelFont());
592 JLabel noText = new JLabel(
593 MessageManager.getString("label.no_value") + COLON);
594 noText.setFont(JvSwingUtils.getLabelFont());
596 colourRangePanel.add(minText);
597 colourRangePanel.add(minColour);
598 colourRangePanel.add(maxText);
599 colourRangePanel.add(maxColour);
600 colourRangePanel.add(noText);
601 colourRangePanel.add(noValueCombo);
604 * third row - threshold options and value
606 JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
607 thresholdPanel.setBackground(Color.white);
608 graduatedColourPanel.add(thresholdPanel);
610 threshold.addActionListener(changeColourAction);
611 threshold.setToolTipText(MessageManager
612 .getString("label.threshold_feature_display_by_score"));
613 threshold.addItem(MessageManager
614 .getString("label.threshold_feature_no_threshold")); // index 0
615 threshold.addItem(MessageManager
616 .getString("label.threshold_feature_above_threshold")); // index 1
617 threshold.addItem(MessageManager
618 .getString("label.threshold_feature_below_threshold")); // index 2
620 thresholdValue.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent e)
625 thresholdValue_actionPerformed();
628 thresholdValue.addFocusListener(new FocusAdapter()
631 public void focusLost(FocusEvent e)
633 thresholdValue_actionPerformed();
636 slider.setPaintLabels(false);
637 slider.setPaintTicks(true);
638 slider.setBackground(Color.white);
639 slider.setEnabled(false);
640 slider.setOpaque(false);
641 slider.setPreferredSize(new Dimension(100, 32));
642 slider.setToolTipText(
643 MessageManager.getString("label.adjust_threshold"));
645 slider.addChangeListener(new ChangeListener()
648 public void stateChanged(ChangeEvent evt)
653 .setText(String.valueOf(slider.getValue() / scaleFactor));
654 thresholdValue.setBackground(Color.white); // to reset red for invalid
655 sliderValueChanged();
659 slider.addMouseListener(new MouseAdapter()
662 public void mouseReleased(MouseEvent evt)
665 * only update Overview and/or structure colouring
666 * when threshold slider drag ends (mouse up)
670 ap.paintAlignment(true, true);
675 thresholdValue.setEnabled(false);
676 thresholdValue.setColumns(7);
678 thresholdPanel.add(threshold);
679 thresholdPanel.add(slider);
680 thresholdPanel.add(thresholdValue);
682 thresholdIsMin.setBackground(Color.white);
684 .setText(MessageManager.getString("label.threshold_minmax"));
685 thresholdIsMin.setToolTipText(MessageManager
686 .getString("label.toggle_absolute_relative_display_threshold"));
687 thresholdIsMin.addActionListener(changeColourAction);
688 thresholdPanel.add(thresholdIsMin);
690 return graduatedColourPanel;
694 * Lay out OK and Cancel buttons
698 private JPanel initialiseOkCancelPanel()
700 JPanel okCancelPanel = new JPanel();
701 // okCancelPanel.setBackground(Color.white);
702 okCancelPanel.add(ok);
703 okCancelPanel.add(cancel);
704 return okCancelPanel;
708 * Lay out Colour options panel, containing
710 * <li>plain colour, with colour picker</li>
711 * <li>colour by text, with choice of Label or other attribute</li>
712 * <li>colour by range, of score or other attribute, when available</li>
717 private JPanel initialiseColoursPanel()
719 JPanel colourByPanel = new JPanel();
720 colourByPanel.setBackground(Color.white);
721 colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
722 JvSwingUtils.createTitledBorder(colourByPanel,
723 MessageManager.getString("action.colour"), true);
726 * simple colour radio button and colour picker
728 JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
729 simpleColourPanel.setBackground(Color.white);
730 colourByPanel.add(simpleColourPanel);
732 simpleColour = new JRadioButton(
733 MessageManager.getString("label.simple_colour"));
734 simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
735 simpleColour.setOpaque(false);
736 simpleColour.addItemListener(new ItemListener()
739 public void itemStateChanged(ItemEvent e)
741 if (simpleColour.isSelected() && !adjusting)
748 singleColour.setFont(JvSwingUtils.getLabelFont());
749 singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
750 singleColour.setPreferredSize(new Dimension(40, 20));
751 if (originalColour.isGraduatedColour())
753 singleColour.setBackground(originalColour.getMaxColour());
754 singleColour.setForeground(originalColour.getMaxColour());
758 singleColour.setBackground(originalColour.getColour());
759 singleColour.setForeground(originalColour.getColour());
761 singleColour.addMouseListener(new MouseAdapter()
764 public void mousePressed(MouseEvent e)
766 if (simpleColour.isSelected())
768 String ttl = MessageManager.formatMessage("label.select_colour_for", featureType);
769 showColourChooser(singleColour, ttl);
773 simpleColourPanel.add(simpleColour); // radio button
774 simpleColourPanel.add(singleColour); // colour picker button
777 * colour by text (category) radio button and drop-down choice list
779 JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
780 byTextPanel.setBackground(Color.white);
781 JvSwingUtils.createTitledBorder(byTextPanel,
782 MessageManager.getString("label.colour_by_text"), true);
783 colourByPanel.add(byTextPanel);
784 byCategory = new JRadioButton(
785 MessageManager.getString("label.by_text_of") + COLON);
786 byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
787 byCategory.setOpaque(false);
788 byCategory.addItemListener(new ItemListener()
791 public void itemStateChanged(ItemEvent e)
793 if (byCategory.isSelected())
799 byTextPanel.add(byCategory);
801 List<String[]> attNames = FeatureAttributes.getInstance()
802 .getAttributes(featureType);
803 colourByTextCombo = populateAttributesDropdown(attNames, false, true);
804 colourByTextCombo.addItemListener(new ItemListener()
807 public void itemStateChanged(ItemEvent e)
812 byTextPanel.add(colourByTextCombo);
815 * graduated colour panel
817 JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
818 colourByPanel.add(graduatedColourPanel);
821 * 3 radio buttons select between simple colour,
822 * by category (text), or graduated
824 ButtonGroup bg = new ButtonGroup();
825 bg.add(simpleColour);
827 bg.add(graduatedColour);
829 return colourByPanel;
833 * Shows a colour chooser dialog, and if a selection is made, updates the
834 * colour of the given panel
837 * the panel whose background colour is being picked
840 void showColourChooser(JPanel colourPanel, String title)
842 ColourChooserListener listener = new ColourChooserListener()
845 public void colourSelected(Color col)
847 colourPanel.setBackground(col);
848 colourPanel.setForeground(col);
849 colourPanel.repaint();
853 JalviewColourChooser.showColourChooser(this, title,
854 colourPanel.getBackground(), listener);
858 * Constructs and sets the selected colour options as the colour for the
859 * feature type, and repaints the alignment, and optionally the Overview
860 * and/or structure viewer if open
862 * @param updateStructsAndOverview
864 void colourChanged(boolean updateStructsAndOverview)
869 * ignore action handlers while setting values programmatically
875 * ensure min-max range is for the latest choice of
876 * 'graduated colour by'
878 updateColourMinMax();
880 FeatureColourI acg = makeColourFromInputs();
883 * save the colour, and repaint stuff
885 fr.setColour(featureType, acg);
886 ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
888 updateColoursPanel();
892 * Converts the input values into an instance of FeatureColour
896 private FeatureColourI makeColourFromInputs()
899 * easiest case - a single colour
901 if (simpleColour.isSelected())
903 return new FeatureColour(singleColour.getBackground());
907 * next easiest case - colour by Label, or attribute text
909 if (byCategory.isSelected())
911 Color c = singleColour.getBackground();
912 FeatureColourI fc = new FeatureColour(c);
913 fc.setColourByLabel(true);
914 String byWhat = (String) colourByTextCombo.getSelectedItem();
915 if (!LABEL_18N.equals(byWhat))
918 FeatureMatcher.fromAttributeDisplayName(byWhat));
924 * remaining case - graduated colour by score, or attribute value
926 Color noColour = null;
927 if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
929 noColour = minColour.getBackground();
931 else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
933 noColour = maxColour.getBackground();
939 thresh = Float.valueOf(thresholdValue.getText());
940 } catch (NumberFormatException e)
942 // invalid inputs are already handled on entry
946 * min-max range is to (or from) threshold value if
947 * 'threshold is min/max' is selected
949 float minValue = min;
950 float maxValue = max;
951 int thresholdOption = threshold.getSelectedIndex();
952 if (thresholdIsMin.isSelected()
953 && thresholdOption == ABOVE_THRESHOLD_OPTION)
957 if (thresholdIsMin.isSelected()
958 && thresholdOption == BELOW_THRESHOLD_OPTION)
964 * make the graduated colour
966 FeatureColourI fc = new FeatureColour(minColour.getBackground(),
967 maxColour.getBackground(), noColour, minValue, maxValue);
970 * set attribute to colour by if selected
972 String byWhat = (String) colourByRangeCombo.getSelectedItem();
973 if (!SCORE_18N.equals(byWhat))
975 fc.setAttributeName(FeatureMatcher.fromAttributeDisplayName(byWhat));
979 * set threshold options and 'autoscaled' which is
980 * false if 'threshold is min/max' is selected
981 * else true (colour range is on actual range of values)
983 fc.setThreshold(thresh);
984 fc.setAutoScaled(!thresholdIsMin.isSelected());
985 fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
986 fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
988 if (threshline == null)
991 * todo not yet implemented: visual indication of feature threshold
993 threshline = new GraphLine((max - min) / 2f, "Threshold",
1001 protected void raiseClosed()
1003 if (this.featureSettings != null)
1005 featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
1010 * Action on OK is just to dismiss the dialog - any changes have already been
1014 public void okPressed()
1019 * Action on Cancel is to restore colour scheme and filters as they were when
1020 * the dialog was opened
1023 public void cancelPressed()
1025 fr.setColour(featureType, originalColour);
1026 fr.setFeatureFilter(featureType, originalFilter);
1027 ap.paintAlignment(true, true);
1031 * Action on text entry of a threshold value
1033 protected void thresholdValue_actionPerformed()
1038 * set 'adjusting' flag while moving the slider, so it
1039 * doesn't then in turn change the value (with rounding)
1042 float f = Float.parseFloat(thresholdValue.getText());
1043 f = Float.max(f, this.min);
1044 f = Float.min(f, this.max);
1045 thresholdValue.setText(String.valueOf(f));
1046 slider.setValue((int) (f * scaleFactor));
1047 threshline.value = f;
1048 thresholdValue.setBackground(Color.white); // ok
1050 colourChanged(true);
1051 } catch (NumberFormatException ex)
1053 thresholdValue.setBackground(Color.red); // not ok
1059 * Action on change of threshold slider value. This may be done interactively
1060 * (by moving the slider), or programmatically (to update the slider after
1061 * manual input of a threshold value).
1063 protected void sliderValueChanged()
1065 threshline.value = getRoundedSliderValue();
1068 * repaint alignment, but not Overview or structure,
1069 * to avoid overload while dragging the slider
1071 colourChanged(false);
1075 * Converts the slider value to its absolute value by dividing by the
1076 * scaleFactor. Rounding errors are squashed by forcing min/max of slider
1077 * range to the actual min/max of feature score range
1081 private float getRoundedSliderValue()
1083 int value = slider.getValue();
1084 float f = value == slider.getMaximum() ? max
1085 : (value == slider.getMinimum() ? min : value / scaleFactor);
1089 void addActionListener(ActionListener listener)
1091 if (featureSettings != null)
1094 "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
1096 featureSettings = listener;
1100 * A helper method to build the drop-down choice of attributes for a feature.
1101 * If 'withRange' is true, then Score, and any attributes with a min-max
1102 * range, are added. If 'withText' is true, Label and any known attributes are
1103 * added. This allows 'categorical numerical' attributes e.g. codon position
1104 * to be coloured by text.
1106 * Where metadata is available with a description for an attribute, that is
1107 * added as a tooltip.
1109 * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ",
1110 * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele.
1112 * This method does not add any ActionListener to the JComboBox.
1118 protected JComboBox<String> populateAttributesDropdown(
1119 List<String[]> attNames, boolean withRange, boolean withText)
1121 List<String> displayAtts = new ArrayList<>();
1122 List<String> tooltips = new ArrayList<>();
1126 displayAtts.add(LABEL_18N);
1127 tooltips.add(MessageManager.getString("label.description"));
1131 float[][] minMax = fr.getMinMax().get(featureType);
1132 if (minMax != null && minMax[0][0] != minMax[0][1])
1134 displayAtts.add(SCORE_18N);
1135 tooltips.add(SCORE_18N);
1139 FeatureAttributes fa = FeatureAttributes.getInstance();
1140 for (String[] attName : attNames)
1142 float[] minMax = fa.getMinMax(featureType, attName);
1143 boolean hasRange = minMax != null && minMax[0] != minMax[1];
1144 if (!withText && !hasRange)
1148 displayAtts.add(FeatureMatcher.toAttributeDisplayName(attName));
1149 String desc = fa.getDescription(featureType, attName);
1150 if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
1152 desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
1154 tooltips.add(desc == null ? "" : desc);
1157 JComboBox<String> attCombo = JvSwingUtils
1158 .buildComboWithTooltips(displayAtts, tooltips);
1164 * Populates initial layout of the feature attribute filters panel
1166 private JPanel initialiseFiltersPanel()
1168 filters = new ArrayList<>();
1170 JPanel filtersPanel = new JPanel();
1171 filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
1172 filtersPanel.setBackground(Color.white);
1173 JvSwingUtils.createTitledBorder(filtersPanel,
1174 MessageManager.getString("label.filters"), true);
1176 JPanel andOrPanel = initialiseAndOrPanel();
1177 filtersPanel.add(andOrPanel);
1180 * panel with filters - populated by refreshFiltersDisplay,
1181 * which also sets the layout manager
1183 chooseFiltersPanel = new JPanel();
1184 chooseFiltersPanel.setBackground(Color.white);
1185 filtersPanel.add(chooseFiltersPanel);
1187 return filtersPanel;
1191 * Lays out the panel with radio buttons to AND or OR filter conditions
1195 private JPanel initialiseAndOrPanel()
1197 JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
1198 andOrPanel.setBackground(Color.white);
1199 andFilters = new JRadioButton(MessageManager.getString("label.and"));
1200 orFilters = new JRadioButton(MessageManager.getString("label.or"));
1201 andFilters.setOpaque(false);
1202 orFilters.setOpaque(false);
1203 ActionListener actionListener = new ActionListener()
1206 public void actionPerformed(ActionEvent e)
1211 andFilters.addActionListener(actionListener);
1212 orFilters.addActionListener(actionListener);
1213 ButtonGroup andOr = new ButtonGroup();
1214 andOr.add(andFilters);
1215 andOr.add(orFilters);
1216 andFilters.setSelected(true);
1218 new JLabel(MessageManager.getString("label.join_conditions")));
1219 andOrPanel.add(andFilters);
1220 andOrPanel.add(orFilters);
1225 * Refreshes the display to show any filters currently configured for the
1226 * selected feature type (editable, with 'remove' option), plus one extra row
1227 * for adding a condition. This should be called after a filter has been
1228 * removed, added or amended.
1230 private void updateFiltersPanel()
1233 * clear the panel and list of filter conditions
1235 chooseFiltersPanel.removeAll();
1239 * look up attributes known for feature type
1241 List<String[]> attNames = FeatureAttributes.getInstance()
1242 .getAttributes(featureType);
1245 * if this feature type has filters set, load them first
1247 FeatureMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
1248 if (featureFilters != null)
1250 if (!featureFilters.isAnded())
1252 orFilters.setSelected(true);
1254 // avoid use of lambda expression to keep SwingJS happy
1255 // featureFilters.getMatchers().forEach(item -> filters.add(item));
1256 for (FeatureMatcherI matcher : featureFilters.getMatchers())
1258 filters.add(matcher);
1263 * and an empty filter for the user to populate (add)
1265 filters.add(FeatureMatcher.NULL_MATCHER);
1268 * use GridLayout to 'justify' rows to the top of the panel, until
1269 * there are too many to fit in, then fall back on BoxLayout
1271 if (filters.size() <= 5)
1273 chooseFiltersPanel.setLayout(new GridLayout(5, 1));
1277 chooseFiltersPanel.setLayout(
1278 new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS));
1282 * render the conditions in rows, each in its own JPanel
1284 int filterIndex = 0;
1285 for (FeatureMatcherI filter : filters)
1287 JPanel row = addFilter(filter, attNames, filterIndex);
1288 chooseFiltersPanel.add(row);
1297 * A helper method that constructs a row (panel) with one filter condition:
1299 * <li>a drop-down list of Label, Score and attribute names to choose
1301 * <li>a drop-down list of conditions to choose from</li>
1302 * <li>a text field for input of a match pattern</li>
1303 * <li>optionally, a 'remove' button</li>
1305 * The filter values are set as defaults for the input fields. The 'remove'
1306 * button is added unless the pattern is empty (incomplete filter condition).
1308 * Action handlers on these fields provide for
1310 * <li>validate pattern field - should be numeric if condition is numeric</li>
1311 * <li>save filters and refresh display on any (valid) change</li>
1312 * <li>remove filter and refresh on 'Remove'</li>
1313 * <li>update conditions list on change of Label/Score/Attribute</li>
1314 * <li>refresh value field tooltip with min-max range on change of
1320 * @param filterIndex
1323 protected JPanel addFilter(FeatureMatcherI filter,
1324 List<String[]> attNames, int filterIndex)
1326 String[] attName = filter.getAttribute();
1327 Condition cond = filter.getMatcher().getCondition();
1328 String pattern = filter.getMatcher().getPattern();
1330 JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
1331 filterRow.setBackground(Color.white);
1334 * drop-down choice of attribute, with description as a tooltip
1335 * if we can obtain it
1337 JComboBox<String> attCombo = populateAttributesDropdown(attNames, true,
1339 String filterBy = setSelectedAttribute(attCombo, filter);
1341 JComboBox<Condition> condCombo = new JComboBox<>();
1343 JTextField patternField = new JTextField(8);
1344 patternField.setText(pattern);
1347 * action handlers that validate and (if valid) apply changes
1349 ActionListener actionListener = new ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 if (validateFilter(patternField, condCombo))
1356 if (updateFilter(attCombo, condCombo, patternField, filterIndex))
1363 ItemListener itemListener = new ItemListener()
1366 public void itemStateChanged(ItemEvent e)
1368 actionListener.actionPerformed(null);
1372 if (filter == FeatureMatcher.NULL_MATCHER) // the 'add a condition' row
1374 attCombo.setSelectedIndex(0);
1378 attCombo.setSelectedItem(
1379 FeatureMatcher.toAttributeDisplayName(attName));
1381 attCombo.addItemListener(new ItemListener()
1384 public void itemStateChanged(ItemEvent e)
1387 * on change of attribute, refresh the conditions list to
1388 * ensure it is appropriate for the attribute datatype
1390 populateConditions((String) attCombo.getSelectedItem(),
1391 (Condition) condCombo.getSelectedItem(), condCombo,
1393 actionListener.actionPerformed(null);
1397 filterRow.add(attCombo);
1400 * drop-down choice of test condition
1402 populateConditions(filterBy, cond, condCombo, patternField);
1403 condCombo.setPreferredSize(new Dimension(150, 20));
1404 condCombo.addItemListener(itemListener);
1405 filterRow.add(condCombo);
1408 * pattern to match against
1410 patternField.addActionListener(actionListener);
1411 patternField.addFocusListener(new FocusAdapter()
1414 public void focusLost(FocusEvent e)
1416 actionListener.actionPerformed(null);
1419 filterRow.add(patternField);
1422 * disable pattern field for condition 'Present / NotPresent'
1424 Condition selectedCondition = (Condition) condCombo.getSelectedItem();
1425 patternField.setEnabled(selectedCondition.needsAPattern());
1428 * if a numeric condition is selected, show the value range
1429 * as a tooltip on the value input field
1431 setNumericHints(filterBy, selectedCondition, patternField);
1434 * add remove button if filter is populated (non-empty pattern)
1436 if (!patternField.isEnabled()
1437 || (pattern != null && pattern.trim().length() > 0))
1439 JButton removeCondition = new JButton("\u2717"); // Dingbats cursive x
1440 removeCondition.setPreferredSize(new Dimension(23, 17));
1442 .setToolTipText(MessageManager.getString("label.delete_row"));
1443 removeCondition.addActionListener(new ActionListener()
1446 public void actionPerformed(ActionEvent e)
1448 filters.remove(filterIndex);
1452 filterRow.add(removeCondition);
1459 * Sets the selected item in the Label/Score/Attribute drop-down to match the
1465 private String setSelectedAttribute(JComboBox<String> attCombo,
1466 FeatureMatcherI filter)
1469 if (filter.isByScore())
1473 else if (filter.isByLabel())
1479 item = FeatureMatcher.toAttributeDisplayName(filter.getAttribute());
1481 attCombo.setSelectedItem(item);
1486 * If a numeric comparison condition is selected, retrieves the min-max range
1487 * for the value (score or attribute), and sets it as a tooltip on the value
1488 * field. If the field is currently empty, then pre-populates it with
1490 * <li>the minimum value, if condition is > or >=</li>
1491 * <li>the maximum value, if condition is < or <=</li>
1495 * @param selectedCondition
1496 * @param patternField
1498 private void setNumericHints(String attName, Condition selectedCondition,
1499 JTextField patternField)
1501 patternField.setToolTipText("");
1503 if (selectedCondition.isNumeric())
1505 float[] minMax = getMinMax(attName);
1508 String minFormatted = DECFMT_2_2.format(minMax[0]);
1509 String maxFormatted = DECFMT_2_2.format(minMax[1]);
1510 String tip = String.format("(%s - %s)", minFormatted, maxFormatted);
1511 patternField.setToolTipText(tip);
1512 if (patternField.getText().isEmpty())
1514 if (selectedCondition == Condition.GE
1515 || selectedCondition == Condition.GT)
1517 patternField.setText(minFormatted);
1521 if (selectedCondition == Condition.LE
1522 || selectedCondition == Condition.LT)
1524 patternField.setText(maxFormatted);
1533 * Populates the drop-down list of comparison conditions for the given
1534 * attribute name. The conditions added depend on the datatype of the
1535 * attribute values. The supplied condition is set as the selected item in the
1536 * list, provided it is in the list. If the pattern is now invalid
1537 * (non-numeric pattern for a numeric condition), it is cleared.
1542 * @param patternField
1544 void populateConditions(String attName, Condition cond,
1545 JComboBox<Condition> condCombo, JTextField patternField)
1547 Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
1548 FeatureMatcher.fromAttributeDisplayName(attName));
1549 if (LABEL_18N.equals(attName))
1551 type = Datatype.Character;
1553 else if (SCORE_18N.equals(attName))
1555 type = Datatype.Number;
1559 * remove itemListener before starting
1561 ItemListener listener = condCombo.getItemListeners()[0];
1562 condCombo.removeItemListener(listener);
1563 boolean condIsValid = false;
1565 condCombo.removeAllItems();
1566 for (Condition c : Condition.values())
1568 if ((c.isNumeric() && type == Datatype.Number)
1569 || (!c.isNumeric() && type != Datatype.Number))
1571 condCombo.addItem(c);
1580 * set the selected condition (does nothing if not in the list)
1584 condCombo.setSelectedItem(cond);
1588 condCombo.setSelectedIndex(0);
1592 * clear pattern if it is now invalid for condition
1594 if (((Condition) condCombo.getSelectedItem()).isNumeric())
1598 String pattern = patternField.getText().trim();
1599 if (pattern.length() > 0)
1601 Float.valueOf(pattern);
1603 } catch (NumberFormatException e)
1605 patternField.setText("");
1610 * restore the listener
1612 condCombo.addItemListener(listener);
1616 * Answers true unless a numeric condition has been selected with a
1617 * non-numeric value. Sets the value field to RED with a tooltip if in error.
1619 * If the pattern is expected but is empty, this method returns false, but
1620 * does not mark the field as invalid. This supports selecting an attribute
1621 * for a new condition before a match pattern has been entered.
1626 protected boolean validateFilter(JTextField value,
1627 JComboBox<Condition> condCombo)
1629 if (value == null || condCombo == null)
1631 return true; // fields not populated
1634 Condition cond = (Condition) condCombo.getSelectedItem();
1635 if (!cond.needsAPattern())
1640 value.setBackground(Color.white);
1641 value.setToolTipText("");
1642 String v1 = value.getText().trim();
1643 if (v1.length() == 0)
1648 if (cond.isNumeric() && v1.length() > 0)
1653 } catch (NumberFormatException e)
1655 value.setBackground(Color.red);
1656 value.setToolTipText(
1657 MessageManager.getString("label.numeric_required"));
1666 * Constructs a filter condition from the given input fields, and replaces the
1667 * condition at filterIndex with the new one. Does nothing if the pattern
1668 * field is blank (unless the match condition is one that doesn't require a
1669 * pattern, e.g. 'Is present'). Answers true if the filter was updated, else
1672 * This method may update the tooltip on the filter value field to show the
1673 * value range, if a numeric condition is selected. This ensures the tooltip
1674 * is updated when a numeric valued attribute is chosen on the last 'add a
1680 * @param filterIndex
1682 protected boolean updateFilter(JComboBox<String> attCombo,
1683 JComboBox<Condition> condCombo, JTextField valueField,
1686 String attName = (String) attCombo.getSelectedItem();
1687 Condition cond = (Condition) condCombo.getSelectedItem();
1688 String pattern = valueField.getText().trim();
1690 setNumericHints(attName, cond, valueField);
1692 if (pattern.length() == 0 && cond.needsAPattern())
1694 valueField.setEnabled(true); // ensure pattern field is enabled!
1699 * Construct a matcher that operates on Label, Score,
1700 * or named attribute
1702 FeatureMatcherI km = null;
1703 if (LABEL_18N.equals(attName))
1705 km = FeatureMatcher.byLabel(cond, pattern);
1707 else if (SCORE_18N.equals(attName))
1709 km = FeatureMatcher.byScore(cond, pattern);
1713 km = FeatureMatcher.byAttribute(cond, pattern,
1714 FeatureMatcher.fromAttributeDisplayName(attName));
1717 filters.set(filterIndex, km);
1723 * Action on any change to feature filtering, namely
1725 * <li>change of selected attribute</li>
1726 * <li>change of selected condition</li>
1727 * <li>change of match pattern</li>
1728 * <li>removal of a condition</li>
1730 * The inputs are parsed into a combined filter and this is set for the
1731 * feature type, and the alignment redrawn.
1733 protected void filtersChanged()
1736 * update the filter conditions for the feature type
1738 boolean anded = andFilters.isSelected();
1739 FeatureMatcherSetI combined = new FeatureMatcherSet();
1741 for (FeatureMatcherI filter : filters)
1743 String pattern = filter.getMatcher().getPattern();
1744 Condition condition = filter.getMatcher().getCondition();
1745 if (pattern.trim().length() > 0 || !condition.needsAPattern())
1749 combined.and(filter);
1753 combined.or(filter);
1759 * save the filter conditions in the FeatureRenderer
1760 * (note this might now be an empty filter with no conditions)
1762 fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
1763 ap.paintAlignment(true, true);
1765 updateFiltersPanel();